Starting phenix.real_space_refine on Fri Aug 22 18:14:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afe_15395/08_2025/8afe_15395.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4124 2.51 5 N 1282 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 1.38, per 1000 atoms: 0.20 Number of scatterers: 6785 At special positions: 0 Unit cell: (63.6, 242.475, 88.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1356 8.00 N 1282 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 271.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 13 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.877A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.591A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.589A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.809A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 463 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2430 1.34 - 1.46: 1083 1.46 - 1.58: 3290 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 6841 Sorted by residual: bond pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.78e+00 bond pdb=" CG1 ILE D 806 " pdb=" CD1 ILE D 806 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C TYR J 832 " pdb=" N VAL J 833 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CB ASN I 869 " pdb=" CG ASN I 869 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" C LYS D 859 " pdb=" N PRO D 860 " ideal model delta sigma weight residual 1.337 1.323 0.014 1.11e-02 8.12e+03 1.49e+00 ... (remaining 6836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 8401 1.17 - 2.34: 683 2.34 - 3.51: 99 3.51 - 4.68: 19 4.68 - 5.85: 7 Bond angle restraints: 9209 Sorted by residual: angle pdb=" N ILE J 806 " pdb=" CA ILE J 806 " pdb=" C ILE J 806 " ideal model delta sigma weight residual 108.93 113.36 -4.43 1.35e+00 5.49e-01 1.08e+01 angle pdb=" N ILE D 806 " pdb=" CA ILE D 806 " pdb=" C ILE D 806 " ideal model delta sigma weight residual 109.30 113.38 -4.08 1.31e+00 5.83e-01 9.70e+00 angle pdb=" C ALA E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta sigma weight residual 120.68 115.81 4.87 1.70e+00 3.46e-01 8.22e+00 angle pdb=" C SER E 112 " pdb=" N ALA E 113 " pdb=" CA ALA E 113 " ideal model delta sigma weight residual 122.42 118.24 4.18 1.55e+00 4.16e-01 7.29e+00 angle pdb=" CA TRP C 827 " pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 113.60 108.52 5.08 1.90e+00 2.77e-01 7.16e+00 ... (remaining 9204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3786 17.25 - 34.51: 381 34.51 - 51.76: 46 51.76 - 69.02: 6 69.02 - 86.27: 14 Dihedral angle restraints: 4233 sinusoidal: 1691 harmonic: 2542 Sorted by residual: dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.73 49.27 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 44.90 48.10 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA HIS A 350 " pdb=" C HIS A 350 " pdb=" N ALA A 351 " pdb=" CA ALA A 351 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 711 0.039 - 0.079: 242 0.079 - 0.118: 79 0.118 - 0.158: 4 0.158 - 0.197: 5 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CB ILE J 842 " pdb=" CA ILE J 842 " pdb=" CG1 ILE J 842 " pdb=" CG2 ILE J 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE I 842 " pdb=" CA ILE I 842 " pdb=" CG1 ILE I 842 " pdb=" CG2 ILE I 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB VAL J 823 " pdb=" CA VAL J 823 " pdb=" CG1 VAL J 823 " pdb=" CG2 VAL J 823 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1038 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 859 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 860 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 417 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN B 417 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN B 417 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 417 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 859 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO J 860 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 860 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 860 " 0.021 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 272 2.71 - 3.26: 6877 3.26 - 3.80: 10416 3.80 - 4.35: 13277 4.35 - 4.90: 22214 Nonbonded interactions: 53056 Sorted by model distance: nonbonded pdb=" O THR B 424 " pdb=" ND2 ASN C 831 " model vdw 2.161 3.120 nonbonded pdb=" NH1 ARG D 799 " pdb=" OG SER D 800 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP I 802 " pdb=" NH2 ARG I 844 " model vdw 2.245 3.120 nonbonded pdb=" NH1 ARG I 808 " pdb=" OH TYR I 810 " model vdw 2.245 3.120 nonbonded pdb=" O ASP C 862 " pdb=" OH TYR C 866 " model vdw 2.255 3.040 ... (remaining 53051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 350 through 445) } ncs_group { reference = (chain 'C' and resid 2 through 887) selection = (chain 'D' and resid 2 through 887) selection = chain 'I' selection = (chain 'J' and resid 2 through 887) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 403 through 441) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6845 Z= 0.272 Angle : 0.700 5.850 9217 Z= 0.430 Chirality : 0.044 0.197 1041 Planarity : 0.004 0.086 1219 Dihedral : 14.166 86.270 2573 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.28), residues: 852 helix: -0.24 (0.25), residues: 379 sheet: -2.06 (0.31), residues: 239 loop : 0.03 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 404 TYR 0.018 0.002 TYR J 13 PHE 0.005 0.001 PHE I 840 TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 6841) covalent geometry : angle 0.69894 ( 9209) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.61102 ( 8) hydrogen bonds : bond 0.21907 ( 459) hydrogen bonds : angle 9.24475 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: C 865 VAL cc_start: 0.7852 (m) cc_final: 0.7637 (p) REVERT: I 862 ASP cc_start: 0.7207 (m-30) cc_final: 0.6998 (m-30) REVERT: J 807 MET cc_start: 0.6494 (mmm) cc_final: 0.5574 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0795 time to fit residues: 12.7878 Evaluate side-chains 116 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 831 ASN C 854 GLN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.178091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167703 restraints weight = 9507.912| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.56 r_work: 0.4064 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3937 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6845 Z= 0.205 Angle : 0.613 7.052 9217 Z= 0.336 Chirality : 0.042 0.172 1041 Planarity : 0.005 0.066 1219 Dihedral : 5.240 24.271 981 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.29 % Allowed : 8.45 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.29), residues: 852 helix: 1.04 (0.26), residues: 386 sheet: -1.93 (0.32), residues: 223 loop : 0.00 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 129 TYR 0.014 0.002 TYR C 13 PHE 0.005 0.001 PHE D 840 TRP 0.009 0.002 TRP I 827 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 6841) covalent geometry : angle 0.61230 ( 9209) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.20571 ( 8) hydrogen bonds : bond 0.05275 ( 459) hydrogen bonds : angle 5.84576 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.266 Fit side-chains REVERT: C 865 VAL cc_start: 0.8162 (m) cc_final: 0.7942 (p) REVERT: E 128 ARG cc_start: 0.6043 (ttm110) cc_final: 0.5784 (ttm170) REVERT: F 143 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7085 (mt) REVERT: H 426 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6957 (mt-10) REVERT: I 817 GLN cc_start: 0.6980 (mp10) cc_final: 0.6622 (mp10) REVERT: I 862 ASP cc_start: 0.7427 (m-30) cc_final: 0.7058 (m-30) REVERT: J 807 MET cc_start: 0.7774 (mmm) cc_final: 0.7439 (mmm) REVERT: J 859 LYS cc_start: 0.7252 (mtmm) cc_final: 0.6966 (mtmm) outliers start: 16 outliers final: 7 residues processed: 114 average time/residue: 0.0864 time to fit residues: 12.8166 Evaluate side-chains 118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 24 optimal weight: 0.0670 chunk 62 optimal weight: 0.0470 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.181789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.171080 restraints weight = 9454.790| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.60 r_work: 0.4103 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6845 Z= 0.120 Angle : 0.489 5.342 9217 Z= 0.271 Chirality : 0.039 0.139 1041 Planarity : 0.004 0.055 1219 Dihedral : 4.577 20.251 981 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.01 % Allowed : 11.03 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.30), residues: 852 helix: 1.99 (0.26), residues: 381 sheet: -1.60 (0.32), residues: 243 loop : 0.56 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.008 0.001 TYR C 13 PHE 0.004 0.001 PHE I 840 TRP 0.007 0.001 TRP D 878 HIS 0.001 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6841) covalent geometry : angle 0.48887 ( 9209) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.73719 ( 8) hydrogen bonds : bond 0.04255 ( 459) hydrogen bonds : angle 5.03053 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.4033 (OUTLIER) cc_final: 0.3620 (m-70) REVERT: E 129 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6788 (ttm-80) REVERT: E 139 ASN cc_start: 0.6138 (t0) cc_final: 0.5780 (t0) REVERT: F 143 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7009 (mt) REVERT: I 817 GLN cc_start: 0.6876 (mp10) cc_final: 0.6565 (mp10) REVERT: J 807 MET cc_start: 0.7725 (mmm) cc_final: 0.7453 (mmm) REVERT: J 859 LYS cc_start: 0.7103 (mtmm) cc_final: 0.6824 (mtmm) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 0.0840 time to fit residues: 12.4975 Evaluate side-chains 114 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.179329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169198 restraints weight = 9425.932| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.53 r_work: 0.4076 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6845 Z= 0.167 Angle : 0.515 4.991 9217 Z= 0.285 Chirality : 0.040 0.138 1041 Planarity : 0.004 0.053 1219 Dihedral : 4.721 21.808 981 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.44 % Allowed : 12.75 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.30), residues: 852 helix: 2.14 (0.25), residues: 382 sheet: -1.66 (0.32), residues: 233 loop : 0.51 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 404 TYR 0.013 0.001 TYR C 13 PHE 0.004 0.001 PHE I 840 TRP 0.007 0.001 TRP J 878 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6841) covalent geometry : angle 0.51421 ( 9209) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.08571 ( 8) hydrogen bonds : bond 0.04346 ( 459) hydrogen bonds : angle 5.03795 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.246 Fit side-chains REVERT: B 367 LEU cc_start: 0.8034 (mp) cc_final: 0.7831 (mt) REVERT: F 143 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7001 (mt) REVERT: H 426 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6843 (mt-10) REVERT: I 872 TYR cc_start: 0.8636 (t80) cc_final: 0.8380 (t80) REVERT: J 807 MET cc_start: 0.7789 (mmm) cc_final: 0.7326 (mmm) REVERT: J 810 TYR cc_start: 0.6627 (m-80) cc_final: 0.6399 (m-80) REVERT: J 859 LYS cc_start: 0.7128 (mtmm) cc_final: 0.6888 (mtmm) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 0.0749 time to fit residues: 11.6528 Evaluate side-chains 119 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.183217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.171935 restraints weight = 9365.210| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.80 r_work: 0.4101 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6845 Z= 0.214 Angle : 0.560 5.663 9217 Z= 0.309 Chirality : 0.041 0.142 1041 Planarity : 0.004 0.051 1219 Dihedral : 4.983 21.717 981 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.58 % Allowed : 13.75 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.30), residues: 852 helix: 2.01 (0.25), residues: 382 sheet: -1.74 (0.31), residues: 244 loop : 0.41 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 128 TYR 0.012 0.002 TYR C 13 PHE 0.004 0.001 PHE I 840 TRP 0.009 0.002 TRP D 878 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 6841) covalent geometry : angle 0.55893 ( 9209) SS BOND : bond 0.00287 ( 4) SS BOND : angle 1.22307 ( 8) hydrogen bonds : bond 0.04575 ( 459) hydrogen bonds : angle 5.17125 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.3993 (OUTLIER) cc_final: 0.3304 (m-70) REVERT: B 367 LEU cc_start: 0.8094 (mp) cc_final: 0.7868 (mt) REVERT: B 397 GLU cc_start: 0.7859 (tp30) cc_final: 0.7527 (tp30) REVERT: E 139 ASN cc_start: 0.6363 (t0) cc_final: 0.6078 (t0) REVERT: F 143 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7108 (mt) REVERT: H 426 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6927 (mt-10) REVERT: I 817 GLN cc_start: 0.7145 (mp10) cc_final: 0.6926 (mp10) REVERT: I 851 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7379 (m) REVERT: J 807 MET cc_start: 0.8074 (mmm) cc_final: 0.7837 (mmm) REVERT: J 810 TYR cc_start: 0.6758 (m-80) cc_final: 0.6500 (m-80) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 0.0868 time to fit residues: 13.5407 Evaluate side-chains 127 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN I 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.183509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172149 restraints weight = 9384.844| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.81 r_work: 0.4102 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6845 Z= 0.201 Angle : 0.549 6.295 9217 Z= 0.303 Chirality : 0.040 0.142 1041 Planarity : 0.004 0.051 1219 Dihedral : 4.945 23.691 981 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.15 % Allowed : 16.05 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 852 helix: 2.00 (0.25), residues: 382 sheet: -1.79 (0.30), residues: 250 loop : 0.42 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.016 0.002 TYR J 13 PHE 0.005 0.001 PHE I 840 TRP 0.011 0.002 TRP D 878 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 6841) covalent geometry : angle 0.54892 ( 9209) SS BOND : bond 0.00212 ( 4) SS BOND : angle 1.00951 ( 8) hydrogen bonds : bond 0.04493 ( 459) hydrogen bonds : angle 5.09997 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.3946 (OUTLIER) cc_final: 0.3259 (m-70) REVERT: B 367 LEU cc_start: 0.8061 (mp) cc_final: 0.7855 (mt) REVERT: B 397 GLU cc_start: 0.7813 (tp30) cc_final: 0.7490 (tp30) REVERT: E 139 ASN cc_start: 0.6358 (t0) cc_final: 0.6032 (t0) REVERT: F 143 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7267 (mt) REVERT: I 851 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7371 (m) REVERT: J 810 TYR cc_start: 0.6760 (m-80) cc_final: 0.6468 (m-80) outliers start: 22 outliers final: 15 residues processed: 122 average time/residue: 0.0748 time to fit residues: 12.1175 Evaluate side-chains 128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 807 MET Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 823 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.183216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172080 restraints weight = 9243.694| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.78 r_work: 0.4104 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6845 Z= 0.207 Angle : 0.561 6.309 9217 Z= 0.309 Chirality : 0.041 0.143 1041 Planarity : 0.004 0.049 1219 Dihedral : 4.981 24.603 981 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.58 % Allowed : 17.19 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.30), residues: 852 helix: 1.97 (0.25), residues: 383 sheet: -1.84 (0.30), residues: 253 loop : 0.39 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.013 0.002 TYR J 13 PHE 0.005 0.001 PHE I 840 TRP 0.013 0.002 TRP D 878 HIS 0.005 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 6841) covalent geometry : angle 0.55981 ( 9209) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.13447 ( 8) hydrogen bonds : bond 0.04531 ( 459) hydrogen bonds : angle 5.12269 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.4060 (OUTLIER) cc_final: 0.3366 (m-70) REVERT: B 397 GLU cc_start: 0.7843 (tp30) cc_final: 0.7524 (tp30) REVERT: E 139 ASN cc_start: 0.6394 (t0) cc_final: 0.6072 (t0) REVERT: F 143 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7284 (mt) REVERT: I 851 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7388 (m) REVERT: J 807 MET cc_start: 0.7959 (mmm) cc_final: 0.7482 (mmp) REVERT: J 810 TYR cc_start: 0.6840 (m-80) cc_final: 0.6470 (m-80) REVERT: J 859 LYS cc_start: 0.7357 (mtmm) cc_final: 0.7088 (mtmm) outliers start: 25 outliers final: 19 residues processed: 120 average time/residue: 0.0782 time to fit residues: 12.4992 Evaluate side-chains 130 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 807 MET Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.172329 restraints weight = 9306.266| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.79 r_work: 0.4100 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6845 Z= 0.181 Angle : 0.542 7.382 9217 Z= 0.297 Chirality : 0.040 0.142 1041 Planarity : 0.003 0.048 1219 Dihedral : 4.850 24.879 981 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.15 % Allowed : 17.91 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.30), residues: 852 helix: 2.13 (0.25), residues: 383 sheet: -1.74 (0.30), residues: 250 loop : 0.42 (0.48), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.012 0.002 TYR C 13 PHE 0.006 0.001 PHE I 840 TRP 0.014 0.001 TRP D 878 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6841) covalent geometry : angle 0.54114 ( 9209) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.95722 ( 8) hydrogen bonds : bond 0.04378 ( 459) hydrogen bonds : angle 5.01596 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.197 Fit side-chains REVERT: A 350 HIS cc_start: 0.3927 (OUTLIER) cc_final: 0.3255 (m-70) REVERT: B 367 LEU cc_start: 0.8050 (mp) cc_final: 0.7823 (mt) REVERT: B 397 GLU cc_start: 0.7827 (tp30) cc_final: 0.7500 (tp30) REVERT: E 139 ASN cc_start: 0.6314 (t0) cc_final: 0.6009 (t0) REVERT: F 143 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7234 (mt) REVERT: I 851 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7337 (m) REVERT: J 807 MET cc_start: 0.7881 (mmm) cc_final: 0.7655 (mmm) REVERT: J 810 TYR cc_start: 0.6840 (m-80) cc_final: 0.6418 (m-80) REVERT: J 859 LYS cc_start: 0.7239 (mtmm) cc_final: 0.6997 (mtmm) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.0800 time to fit residues: 12.3206 Evaluate side-chains 128 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.183698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.172419 restraints weight = 9277.585| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.79 r_work: 0.4104 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6845 Z= 0.173 Angle : 0.545 7.037 9217 Z= 0.298 Chirality : 0.040 0.141 1041 Planarity : 0.003 0.048 1219 Dihedral : 4.775 23.007 981 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.87 % Allowed : 17.48 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.30), residues: 852 helix: 2.19 (0.25), residues: 383 sheet: -1.75 (0.30), residues: 253 loop : 0.49 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.013 0.002 TYR D 872 PHE 0.007 0.001 PHE I 840 TRP 0.011 0.001 TRP D 878 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6841) covalent geometry : angle 0.54443 ( 9209) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.97271 ( 8) hydrogen bonds : bond 0.04327 ( 459) hydrogen bonds : angle 4.96875 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.182 Fit side-chains REVERT: A 350 HIS cc_start: 0.4046 (OUTLIER) cc_final: 0.3443 (m-70) REVERT: B 367 LEU cc_start: 0.8034 (mp) cc_final: 0.7815 (mt) REVERT: B 397 GLU cc_start: 0.7823 (tp30) cc_final: 0.7501 (tp30) REVERT: E 128 ARG cc_start: 0.6033 (ttm110) cc_final: 0.5807 (ttm170) REVERT: E 139 ASN cc_start: 0.6304 (t0) cc_final: 0.6009 (t0) REVERT: F 143 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7256 (mt) REVERT: I 851 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7353 (m) REVERT: J 807 MET cc_start: 0.7907 (mmm) cc_final: 0.7631 (mmm) REVERT: J 810 TYR cc_start: 0.6864 (m-80) cc_final: 0.6478 (m-80) REVERT: J 859 LYS cc_start: 0.7236 (mtmm) cc_final: 0.6997 (mtmm) outliers start: 27 outliers final: 21 residues processed: 121 average time/residue: 0.0741 time to fit residues: 11.9922 Evaluate side-chains 129 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 76 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 55 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 9 optimal weight: 0.0970 chunk 82 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.184006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.172163 restraints weight = 9545.390| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.91 r_work: 0.4092 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6845 Z= 0.131 Angle : 0.504 8.432 9217 Z= 0.276 Chirality : 0.038 0.138 1041 Planarity : 0.004 0.047 1219 Dihedral : 4.515 22.089 981 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.15 % Allowed : 18.05 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.31), residues: 852 helix: 2.46 (0.25), residues: 381 sheet: -1.60 (0.31), residues: 253 loop : 0.79 (0.50), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 404 TYR 0.011 0.001 TYR I 872 PHE 0.007 0.001 PHE I 840 TRP 0.014 0.001 TRP D 878 HIS 0.002 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6841) covalent geometry : angle 0.50419 ( 9209) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.71144 ( 8) hydrogen bonds : bond 0.04034 ( 459) hydrogen bonds : angle 4.77235 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.211 Fit side-chains REVERT: A 350 HIS cc_start: 0.3544 (OUTLIER) cc_final: 0.3069 (m-70) REVERT: B 367 LEU cc_start: 0.7973 (mp) cc_final: 0.7750 (mt) REVERT: B 397 GLU cc_start: 0.7802 (tp30) cc_final: 0.7479 (tp30) REVERT: B 404 ARG cc_start: 0.7119 (ptt-90) cc_final: 0.6860 (mtm-85) REVERT: E 128 ARG cc_start: 0.6064 (ttm110) cc_final: 0.5834 (ttm170) REVERT: H 426 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7088 (mt-10) REVERT: H 429 LEU cc_start: 0.8383 (mm) cc_final: 0.8113 (mp) REVERT: I 851 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7334 (m) REVERT: I 872 TYR cc_start: 0.8576 (t80) cc_final: 0.8357 (t80) REVERT: J 807 MET cc_start: 0.7781 (mmm) cc_final: 0.7406 (mmm) REVERT: J 810 TYR cc_start: 0.6831 (m-80) cc_final: 0.6437 (m-80) REVERT: J 859 LYS cc_start: 0.7018 (mtmm) cc_final: 0.6771 (mtmm) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.0748 time to fit residues: 11.7401 Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.185999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174109 restraints weight = 9479.735| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.91 r_work: 0.4112 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6845 Z= 0.115 Angle : 0.492 8.221 9217 Z= 0.267 Chirality : 0.038 0.149 1041 Planarity : 0.003 0.046 1219 Dihedral : 4.261 18.772 981 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.72 % Allowed : 18.48 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.31), residues: 852 helix: 2.53 (0.25), residues: 393 sheet: -1.50 (0.31), residues: 253 loop : 0.92 (0.52), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 404 TYR 0.011 0.001 TYR I 872 PHE 0.006 0.001 PHE I 840 TRP 0.014 0.001 TRP D 878 HIS 0.001 0.000 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 6841) covalent geometry : angle 0.49179 ( 9209) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.57481 ( 8) hydrogen bonds : bond 0.03839 ( 459) hydrogen bonds : angle 4.56248 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.26 seconds wall clock time: 29 minutes 15.56 seconds (1755.56 seconds total)